Exactly.
As one example, whilst things are much better than they were, there are still bigots about and there is an increased chance of being attacked simply for holding hands with your lover if they are the same gender and that is something many parents just wouldn't want their child to face.
Also, again, better than it was with same sex marriage, gay adoption allowed and IVF enabling SuRrogacy but until recently there was the issue of not having grand children or see their child in a secure, long term relationship. Again, something most parents would want for their child.
So, I'm not sure that all parents that initially struggle with their children coming out should be condemned as homophobic.
However in Phil's case, I don't think it is that as much as what he has been conditioned by his upbringing to think a 'real man' should be.
I don't think it is his age (mid 50s really isn't that old, things were changing when he was still quite young - I'm in my mid 40s, i have loads of friends mid to late 50s who aren't homophobic and indeed were friends with gay people so involved with the culture during the 70s and 80s) but it is the way he was brought up by Eric.